The initiation events in programmed cell death are being investigated by preparation of soluble complexes of death domains and death effector domains. Limited proteolysis and mass spectrometry analysis have been applied to the FADD, FLIP, FAS, RIP and TRADD proteins to define the functional domains and construct suitable overexpressing clones to study the structure of interacting segments of these molecules. The aforementioned proteins receive signals from a subset of tumor necrosis factor receptors (TNFRs) that contain a death domain. A second class of TNFRs interact with theTRAF molecules to transmit a signal that leads to cell proliferation instead of cell death. Mass spec and Western blot analysis have been applied to TRAF2 to define the minimal interacting domain, to define the interaction surface of CD30 and CD40 in preparation for a full structural analysis of a TRAF/receptor domain complex.